Introdouction: The high prevalence of apical periodontitis (AP) of endodontic origin raises an important public health problem. Root canal treatment (RCT) and crown restoration (CR) have an effect on its prevalence. This cross-sectional study was performed to assess the effect of RCT and CR on the prevalence of AP.Materials and methods: Two observers assessed 608 teeth with RCT belonging to patients who were referred to the radiology ward of the dental school at the Shahid Sadoughi University of Medical Sciences, Yazd, Iran, in 2011–2012 in the form of 152 panoramic radiographs. The quality of RCT, including length/ density of root restoration, and crown restoration and the prevalence of AP were recorded from patients’ medical files. Data were analyzed by chi-square test, one-way ANOVA, and logistic regression model using SPSS (ver. 19).Results:The frequency of AP in teeth with RCT was 50.5%. Appropriate CR and RCT was observed in 348 (57.2%) and 168 (30.6%) of teeth, respectively. Furthermore, 36.8% of teeth with appropriate and 68.8% with inappropriate crown restoration showed AP, and the difference was significant (p < 0.001). Prevalence of AP was significantly lower in teeth with acceptable RCT than in those with unacceptable RCT (p < 0.001). Teeth with unacceptable RCT/CR showed AP 6 times more frequently than teeth with acceptable RCT/CR.Conclusion: The findings showed that a considerable number of teeth in Yazd had RCT/CR with unacceptable results and that the quality of both RCT and CR may affect the prevalence of AP. Therefore, considerable efforts are required to improve endodontic and restorative treatment standards.